This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The mechanisms for ion-molecule reactions and fragmentation of small ions that have biological significance are being explored by ab initio and density functional methods. The calculations are executed to obtain thermochemical information, structures, and transition states for fragmentation processes, along with ion-molecule reactions of various small molecule ions and their subsequent patterns of fragmentation. To carry out this work, we have set up a small cluster of Dell computers, which we have expanded in this cycle, that are devoted to these calculations. When needed, we couple the theoretical work with experiments using MS/MS (ion trap, three sector, four sector), kinetic-energy release, isotope labeling, reactivity correlation, and other tools that are important in mechanism studies. This is a unique area of research for Research Resources in the mass spectrometry area, and our goal is to provide a resource for solving interesting mass spectral fragmentation problems that apply to biological molecules.